make_ligand_activity_target_exprs_plot

make_ligand_activity_target_exprs_plot Plot the ligand expression in senders plus their activity and target genes in receivers

Usage

make_ligand_activity_target_exprs_plot(receiver_oi, prioritized_tbl_oi, prioritization_tbl_ligand_receptor, prioritization_tbl_ligand_target,
exprs_tbl_ligand, exprs_tbl_target, lfc_cutoff, ligand_target_matrix, scaled_ligand_activity_limits = "abs_max", plot_legend = TRUE, heights = NULL, widths = NULL)

Arguments

receiver_oi

Name of the receiver cell type of interest

prioritized_tbl_oi

Dataframe with the ligand-receptor interactions that should be visualized

prioritization_tbl_ligand_receptor

$prioritization_tbl_ligand_receptor slot of `get_prioritization_tables`

prioritization_tbl_ligand_target

$prioritization_tbl_ligand_target slot of `get_prioritization_tables`

exprs_tbl_ligand

Dataframe with the expression values for the ligands in the sender cell types

exprs_tbl_target

Dataframe with the expression values for the targets in the receiver cell types

lfc_cutoff

Cutoff used on the logFC value

ligand_target_matrix

ligand-target matrix

scaled_ligand_activity_limits

limits used in the heatmap for the scaled ligand activity, one of "abs_max" (-+ absolute maximum), "min_max" (minimum and maximum), or "IQR" (cf. boxplot, outliers are squished to the limits)

plot_legend

TRUE (default): add legend to the plot. FALSE: do not add legend.

heights

automatic determination if default NULL. If not NULL: number given by the user to indicate the requested heights, which are the height proportions of the different row panels in the plot.

widths

automatic determination if default NULL. If not NULL: number given by the user to indicate the requested widths, which are the width proportions of the different columns (side-by-side heatmaps) in the plot.

Value

List containing the combined heatmap and the legend

Examples

if (FALSE) { # \dontrun{
make_ligand_activity_target_exprs_plot(receiver_oi, prioritized_tbl_oi, prioritization_tbl_ligand_receptor, prioritization_tbl_ligand_target, exprs_tbl_ligand, exprs_tbl_target, lfc_cutoff, ligand_target_matrix, scaled_ligand_activity_limits = "abs_max", plot_legend = TRUE, heights = NULL, widths = NULL)
} # }